HDNA methylation data-based molecular subtype classification related to the prognosis of patients with hepatocellular ca
- PDF / 5,787,397 Bytes
- 11 Pages / 595.276 x 790.866 pts Page_size
- 104 Downloads / 176 Views
RESEARCH ARTICLE
Open Access
HDNA methylation data-based molecular subtype classification related to the prognosis of patients with hepatocellular carcinoma Hui He1†, Di Chen2†, Shimeng Cui3†, Gang Wu4, Hailong Piao2, Xun Wang1, Peng Ye5 and Shi Jin1*
Abstract Background: DNA methylation is a common chemical modification of DNA in the carcinogenesis of hepatocellular carcinoma (HCC). Methods: In this bioinformatics analysis, 348 liver cancer samples were collected from the Cancer Genome Atlas (TCGA) database to analyse specific DNA methylation sites that affect the prognosis of HCC patients. Results: 10,699 CpG sites (CpGs) that were significantly related to the prognosis of patients were clustered into 7 subgroups, and the samples of each subgroup were significantly different in various clinical pathological data. In addition, by calculating the level of methylation sites in each subgroup, 119 methylation sites (corresponding to 105 genes) were selected as specific methylation sites within the subgroups. Moreover, genes in the corresponding promoter regions in which the above specific methylation sites were located were subjected to signalling pathway enrichment analysis, and it was discovered that these genes were enriched in the biological pathways that were reported to be closely correlated with HCC. Additionally, the transcription factor enrichment analysis revealed that these genes were mainly enriched in the transcription factor KROX. A naive Bayesian classification model was used to construct a prognostic model for HCC, and the training and test data sets were used for independent verification and testing. Conclusion: This classification method can well reflect the heterogeneity of HCC samples and help to develop personalized treatment and accurately predict the prognosis of patients. Keywords: DNA methylation, Molecular subtype classification, TCGA database, Hepatocellular carcinoma
* Correspondence: [email protected] † Hui He, Di Chen and Shimeng Cui contributed equally to this work. 1 Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Lianhe Road 193#, Shahekou District, Dalian 116000, Liaoning Province, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright hol
Data Loading...
